
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  selected   64 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        3.30     3.30
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      60_A - 85_A        1.98     3.69
  LCS_AVERAGE:     33.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      69_A - 85_A        0.79     3.92
  LCS_AVERAGE:     20.09

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     A    22_A     A    22_A      3    3   64      3    3    7    7   12   17   28   44   58   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      3    4   10   17   20   25   34   52   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   17   64      3    5   18   32   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     14   17   64      4    4    8   27   34   41   45   51   57   59   61   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     14   17   64      4   25   31   34   38   43   49   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     14   17   64     12   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     14   17   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     14   17   64     17   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     14   17   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     14   17   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     14   17   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     14   17   64     14   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     14   17   64     13   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     14   17   64      7   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     14   17   64      5   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     14   17   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     14   17   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     14   17   64      3    5   16   33   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A      4   17   64      4    5    6   17   21   29   49   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A      4   17   64      4    5    6   12   16   22   33   45   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      4   17   64      4    4   10   20   30   37   43   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      4   20   64      4    4    7   17   29   37   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      7   20   64      4    5    8   15   18   19   22   27   31   51   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A      7   20   64      4    4   12   17   20   33   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A      7   21   64      4    5   10   17   20   30   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     16   21   64      4    8   13   17   20   23   36   50   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     16   21   64      4   14   15   16   18   23   30   49   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     16   21   64     10   14   15   17   20   34   49   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     16   21   64     10   14   15   17   20   38   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     16   21   64     10   14   15   16   23   41   49   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     16   21   64      7   14   15   31   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     16   21   64      9   14   19   32   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     16   21   64     10   14   15   17   37   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     16   21   64     10   14   15   18   37   42   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     16   21   64     10   14   23   32   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     16   21   64     10   14   25   32   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     16   21   64     10   14   15   17   23   42   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     16   21   64     10   14   15   17   21   38   49   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     16   26   64     10   14   15   17   23   42   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     16   26   64      6   14   15   30   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     16   26   64      3   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A      4   26   64      3    3   23   34   37   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A      4   26   64     12   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A      4   26   64      5   25   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      3   26   64      3    3   15   29   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A      3   26   64      3    3    6   15   23   42   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A      4   26   64      4    4    5    6   28   34   44   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     17   26   64      4    5   21   34   38   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     17   26   64      4   11   16   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     17   26   64     15   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     17   26   64     10   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     17   26   64     10   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     17   26   64     18   29   31   34   39   43   50   54   59   62   63   63   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  51.10  (  20.09   33.20  100.00 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_AT     18     29     31     34     39     43     50     54     59     62     63     63     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  28.12  45.31  48.44  53.12  60.94  67.19  78.12  84.38  92.19  96.88  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.38   0.56   0.63   0.86   1.53   1.67   2.33   2.54   2.93   3.14   3.26   3.18   3.30   3.30   3.30   3.30   3.30   3.30   3.30   3.30
GDT RMS_ALL_AT   3.88   3.89   3.91   3.89   3.67   3.67   3.47   3.40   3.31   3.30   3.30   3.30   3.30   3.30   3.30   3.30   3.30   3.30   3.30   3.30

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     7.888     0    0.078   0.077     9.786   10.119    8.190
LGA    D    23_A      D    23_A     7.025     0    0.146   0.283    10.723   19.405   10.655
LGA    G    24_A      G    24_A     2.304     0    0.451   0.451     4.118   56.667   56.667
LGA    D    25_A      D    25_A     4.159     0    0.722   1.293     8.646   50.833   28.690
LGA    G    26_A      G    26_A     2.437     0    0.173   0.173     3.223   65.119   65.119
LGA    Q    27_A      Q    27_A     1.708     0    0.063   0.571     2.346   72.857   70.159
LGA    G    28_A      G    28_A     1.666     0    0.040   0.040     1.703   77.143   77.143
LGA    L    29_A      L    29_A     1.512     0    0.041   0.234     2.211   75.000   73.988
LGA    Y    30_A      Y    30_A     1.330     0    0.046   0.152     1.463   81.429   81.429
LGA    A    31_A      A    31_A     1.454     0    0.056   0.054     1.673   81.429   79.714
LGA    A    32_A      A    32_A     1.250     0    0.113   0.110     1.374   81.429   81.429
LGA    N    33_A      N    33_A     1.362     0    0.156   0.183     2.253   75.119   74.048
LGA    C    34_A      C    34_A     1.183     0    0.028   0.163     1.458   81.429   82.937
LGA    A    35_A      A    35_A     2.062     0    0.040   0.043     2.441   66.786   66.381
LGA    A    36_A      A    36_A     2.074     0    0.077   0.075     2.074   70.833   69.619
LGA    C    37_A      C    37_A     1.596     0    0.040   0.047     1.697   72.857   75.714
LGA    H    38_A      H    38_A     1.754     0    0.635   1.227     4.643   65.476   61.524
LGA    G    39_A      G    39_A     2.032     0    0.235   0.235     2.813   67.024   67.024
LGA    A    40_A      A    40_A     5.265     0    0.226   0.284     6.370   26.548   24.667
LGA    L    41_A      L    41_A     6.108     0    0.061   1.396    10.522   20.357   14.405
LGA    A    42_A      A    42_A     5.398     0    0.084   0.080     5.519   25.000   25.238
LGA    T    43_A      T    43_A     4.738     0    0.602   1.379     7.001   25.357   22.857
LGA    S    44_A      S    44_A     8.276     0    0.646   0.578    11.523   11.190    7.460
LGA    E    45_A      E    45_A     4.573     0    0.205   1.120     7.112   33.333   27.619
LGA    K    46_A      K    46_A     4.211     0    0.259   1.322    12.538   32.976   18.413
LGA    K    47_A      K    47_A     6.308     0    0.047   1.291    14.670   22.738   11.746
LGA    G    48_A      G    48_A     6.986     0    0.230   0.230     6.986   17.381   17.381
LGA    T    49_A      T    49_A     4.525     0    0.173   1.145     6.889   32.976   31.361
LGA    T    50_A      T    50_A     4.035     0    0.048   1.089     4.978   40.238   45.034
LGA    L    51_A      L    51_A     4.283     0    0.032   1.023     9.191   40.238   26.369
LGA    A    52_A      A    52_A     2.672     0    0.043   0.051     3.118   59.167   60.286
LGA    R    53_A      R    53_A     1.822     0    0.035   1.464     6.943   70.833   52.944
LGA    L    54_A      L    54_A     3.009     0    0.025   1.145     5.864   51.786   46.726
LGA    Q    55_A      Q    55_A     3.462     0    0.037   1.245     3.611   50.000   56.190
LGA    S    56_A      S    56_A     2.277     0    0.086   0.083     2.730   62.857   66.190
LGA    A    57_A      A    57_A     1.697     0    0.028   0.041     2.495   68.810   71.333
LGA    V    58_A      V    58_A     3.744     0    0.030   1.139     6.717   41.905   37.347
LGA    S    59_A      S    59_A     4.419     0    0.131   0.767     6.712   35.952   32.381
LGA    A    60_A      A    60_A     3.712     0    0.325   0.328     4.856   40.357   42.286
LGA    N    61_A      N    61_A     2.555     0    0.611   1.229     4.181   55.595   53.869
LGA    A    62_A      A    62_A     1.863     0    0.222   0.256     3.247   66.905   63.524
LGA    G    63_A      G    63_A     2.883     0    0.557   0.557     2.883   71.071   71.071
LGA    G    64_A      G    64_A     2.474     0    0.104   0.104     2.526   62.857   62.857
LGA    M    65_A      M    65_A     2.045     0    0.721   0.772     3.673   63.095   58.452
LGA    G    66_A      G    66_A     2.451     0    0.624   0.624     2.451   66.786   66.786
LGA    F    67_A      F    67_A     3.715     0    0.372   1.019     4.973   40.357   48.745
LGA    L    68_A      L    68_A     4.554     0    0.268   1.424    11.273   42.024   23.393
LGA    S    69_A      S    69_A     2.889     0    0.137   0.128     3.336   57.262   57.302
LGA    S    70_A      S    70_A     2.014     0    0.160   0.676     2.733   70.952   67.619
LGA    L    71_A      L    71_A     0.967     0    0.063   0.965     3.172   85.952   80.952
LGA    T    72_A      T    72_A     1.520     0    0.069   0.085     1.596   75.000   77.755
LGA    S    73_A      S    73_A     1.823     0    0.040   0.640     2.077   72.857   71.508
LGA    A    74_A      A    74_A     1.477     0    0.053   0.054     1.549   79.286   79.714
LGA    Q    75_A      Q    75_A     1.136     0    0.064   0.240     1.271   81.429   85.450
LGA    L    76_A      L    76_A     1.454     0    0.056   0.942     3.258   81.429   74.286
LGA    Q    77_A      Q    77_A     1.256     0    0.028   1.048     6.464   81.429   60.952
LGA    A    78_A      A    78_A     1.345     0    0.024   0.033     1.363   81.429   81.429
LGA    I    79_A      I    79_A     1.249     0    0.031   0.689     1.503   81.429   81.488
LGA    V    80_A      V    80_A     0.986     0    0.027   1.216     3.297   83.690   77.143
LGA    D    81_A      D    81_A     0.994     0    0.046   0.339     1.313   85.952   87.083
LGA    V    82_A      V    82_A     1.673     0    0.110   0.097     1.975   77.143   75.306
LGA    L    83_A      L    83_A     1.563     0    0.167   0.234     2.008   72.857   73.988
LGA    A    84_A      A    84_A     1.567     0    0.106   0.104     1.950   72.857   74.571
LGA    V    85_A      V    85_A     1.645     0    0.537   0.441     3.200   67.143   69.660

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     3.297          3.212                  3.976           58.715   56.149

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     54    2.54    70.703    64.564     2.047

LGA_LOCAL      RMSD:   2.538  Number of atoms:   54  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.401  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.297  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.139272 * X  +   0.745210 * Y  +  -0.652124 * Z  +  79.260780
  Y_new =  -0.916222 * X  +  -0.152868 * Y  +  -0.370363 * Z  +  78.451378
  Z_new =  -0.375687 * X  +   0.649072 * Y  +   0.661487 * Z  + -34.706154 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.419945  0.385137  0.775925   [DEG:  -81.3568   22.0668   44.4572 ]
ZXZ: -1.054290  0.847996 -0.524690   [DEG:  -60.4063   48.5866  -30.0625 ]
 
# END of job
